During the Civil War, Harpers Ferry changed hands eight times. The most dramatic moment came in September 1862, when Confederate Gen. "Stonewall" Jackson captured 12,500 Union soldiers—the largest surrender of Union troops during the war.

Throughout the war, Harpers Ferry suffered heavy damage. Fighting, looting, and guerrilla attacks left the town in ruins. Buildings were destroyed, streets filled with trash, and the railroad bridge was rebuilt nine times. Despite the destruction, the town slowly recovered after the war.